output_definition.json

{
  "files": {
    "workflow-report": {
      "filepath": "./wf-amplicon-report.html",
      "title": "workflow report",
      "description": "Report for all samples.",
      "mime-type": "text/html",
      "optional": false,
      "type": "aggregated"
    },
    "sanitized-ref": {
      "filepath": "./reference_sanitized_seqIDs.fasta",
      "title": "Sanitized reference file",
      "description": "Some programs used by the workflow don't like special characters (like colons) in the sequence IDs in the reference FASTA file. The reference is thus \"sanitized\" by replacing these characters with underscores. This file is only generated when the workflow is run in variant calling mode.",
      "mime-type": "text/txt",
      "optional": true,
      "type": "aggregated"
    },
    "alignments": {
      "filepath": "./{{ alias }}/alignments/aligned.sorted.bam",
      "title": "Alignments BAM file",
      "description": "BAM file with alignments of input reads against the references (in variant calling mode) or the created consensus (in de-novo consensus mode).",
      "mime-type": "application/gzip",
      "optional": false,
      "type": "per-sample"
    },
    "alignments-index": {
      "filepath": "./{{ alias }}/alignments/aligned.sorted.bam.bai",
      "title": "Alignments index file",
      "description": "Index for alignments BAM file.",
      "mime-type": "application/octet-stream",
      "optional": false,
      "type": "per-sample"
    },
    "consensus-fastq": {
      "filepath": "./{{ alias }}/consensus/consensus.fastq",
      "title": "De-novo consensus FASTQ file",
      "description": "Consensus file generated by de-novo consensus pipeline.",
      "mime-type": "text/txt",
      "optional": true,
      "type": "per-sample"
    },
    "consensus-fasta": {
      "filepath": "./{{ alias }}/consensus/consensus.fasta",
      "title": "Consensus FASTA file",
      "description": "Consensus file generated variant calling pipeline.",
      "mime-type": "text/txt",
      "optional": true,
      "type": "per-sample"
    },
    "variants": {
      "filepath": "./{{ alias }}/variants/medaka.annotated.vcf.gz",
      "title": "Variants VCF file",
      "description": "VCF file of variants detected against the provided reference.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    },
    "variants-index": {
      "filepath": "./{{ alias }}/variants/medaka.annotated.vcf.gz.csi",
      "title": "Variants index file",
      "description": "Index for variants VCF file.",
      "mime-type": "application/gzip",
      "optional": true,
      "type": "per-sample"
    }
  }
}